Changeset 737

Timestamp:

Aug 7, 2008, 9:07:42 AM (14 years ago)

Author:

Martin Svensson

Message:

Fixes #121 BGX-importer should 0-pad Array_Address_ID if the BGX-file doesn't have done that already.
Also changed some version-tags to hold the correct number.

Location:

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina

Files:

• Illumina.java (modified) (1 diff)
• plugins/BgxFeatureImporter.java (modified) (3 diffs)
• plugins/ZeroPadMapper.java (added)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/Illumina.java

@@ -36 +36 @@
     The current version of this plug-in package.
   */
-  public static final String VERSION = "pre1.1";
+  public static final String VERSION = "pre1.2";
   
   /**

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BgxFeatureImporter.java

@@ -43 +43 @@
 import net.sf.basedb.util.InputStreamTracker;
 import net.sf.basedb.util.parser.FlatFileParser;
+import net.sf.basedb.util.parser.Mapper;
 import net.sf.basedb.util.parser.WrappedConfigureByExample;
 import net.sf.basedb.util.parser.FlatFileParser.Line;
@@ -63 +64 @@
   
   @author Martin, Nicklas
-  @version 2.6
+  @version 1.0
 
 */
@@ -187 +188 @@
   }
   
+  
+  
+  /**
+    This method returns a ZeroPadMapper if the mapp-expression is equal to '\\Array_Address_Id\\', 
+    otherwise the object from it's super class will be returned.
+    @see net.sf.basedb.plugins.AbstractFlatFileImporter#getMapper()
+    @see net.sf.basedb.illumina.plugins.ZeroPadMapper
+    @since 1.2
+   */
+  @Override
+  protected Mapper getMapper(FlatFileParser ffp, String mapExpression, Integer maxStringLength, Mapper defaultMapper)
+  {
+    Mapper mapper = super.getMapper(ffp, mapExpression, maxStringLength, defaultMapper);
+    
+    if (mapExpression != null && mapExpression.equals("\\Array_Address_Id\\"))
+    {
+      mapper = new ZeroPadMapper(mapper, 10);
+    }
+    return mapper;
+  }
   /*
     Enum to hold the sections in a BGX file.